Alex Rolfe

Research

Computational
Genomics Group at
MIT CSAIL. My research
focused on the genetic regulatory networks of pancreatic development
as part of the SysCODE Project.
We used ChIP-Seq (detects protein-DNA interactions), gene expression data,
and proteomics data (protein-protein interactions and protein
abundance) to understand the steps in development as cells go from
stem cells to endoderm and hopefully to pancreatic beta cells.

ReadDB, a custom
column store database system for short reads (eg, Illumina/Solexa,
ABI/SOLiD) that have been mapped to a genome. We currently store
several thousand lanes of sequencing data in this system to support
ChIP-Seq and RNA-Seq analysis and visualization.

Ruler
Arrays, a novel method to detect structural variants between two
genomes.

GSE, a
database and codebase for genomic analysis. This is the shared Java
environment that our group uses.

Joint Binding
Deconvolution
(pubmed), a
method for analyzing ChIP-Chip data that improves the spatial accuracy
of the resulting protein-DNA interaction predictions and can detect
pairs of closely spaced interactions.

Everything Else

LSC: On campus movie theater
and lecture series. I have served as Chairman, Treasurer, Publicity
director, and Projection director. I've
seen a
lot of movies and annoy my family with high standards for 35mm
projection.

I've volunteered
for Hub on Wheels for
several years. This annual ride has 10, 30, and 50 mile loops
from Government Center.
The 30
mile and
50 mile routes are a fantastic tour of the southern parts of
Boston including Forest Hills Cemetary, the Arnold Arboretum, and
the waterfront.